predictEnmSdm {enmSdmX}R Documentation

Generic predict function for SDMs/ENMs

Description

This is a generic predict function that automatically uses the model common arguments for predicting models of the following types: linear models, generalized linear models (GLMs), generalized additive models (GAMs), random forests, boosted regression trees (BRTs)/gradient boosting machines (GBMs), conditional random forests, MaxEnt, and more.

Usage

predictEnmSdm(
  model,
  newdata,
  maxentFun = "terra",
  scale = TRUE,
  cores = 1,
  nrows = nrow(newdata),
  paths = .libPaths(),
  ...
)

Arguments

model

Object of class lm, glm, gam, randomForest, MaxEnt, maxnet, prcomp, kde, gbm, and possibly others (worth a try!).

newdata

Data frame or matrix, or SpatRaster with data to which to predict.

maxentFun

This argument is only used if the model object is a MaxEnt model; otherwise, it is ignored. It takes a value of either 'terra', in which case a MaxEnt model is predicted using the default predict function from the terra package, or 'enmSdmX' in which case the function predictMaxEnt function from the enmSdmX package (this package) is used.

scale

Logical. If the model is a GLM trained with trainGLM, you can use the scale argument in that function to center and scale the predictors. In the predictEnmSdm function, you can set scale to TRUE to scale the rasters or data frame to which you are training using the centers (means) and scales (standard deviations) used in the mode. Otherwise, it is up to you to ensure variables are properly centered and scaled. This argument only has effect if the model is a GLM trained using trainGLM.

cores

Integer >= 1. Number of cores to use when calculating multiple models. Default is 1. This is forced to 1 if newdata is a SpatRaster (i.e., as of now, there is no parallelization when predicting to a raster... sorry!). If you have issues when cores > 1, please see the troubleshooting_parallel_operations guide.

nrows

Number of rows of newdata to predict at a time. This is only used if newdata is a data.frame or matrix. The default is to predict all rows at once, but for very large data frames/matrices this can lead to memory issues in some cases. By setting the number of rows, newdata is divided into chunks, and predictions made to each chunk, which may ease memory limitations. This can be combined with multi-coring (which will increase memory requirements). In this case, all cores combined will get nrows of data. How many rows are too many? You will have to decide depending on the capabilities of your system. For example, predicting the outcome of a GLM on data with 10E6 rows may be fine, but predicting a PCA (with multiple axes) to the data data may require too much memory.

paths

Locations where packages are stored. This is typically not useful to the general user, and is only supplied for when the function is called as a functional.

...

Arguments to pass to the algorithm-specific predict function.

Value

Numeric or SpatRaster.

See Also

predict from the stats package, predict from the terra package, predictMaxEnt, predictMaxNet

Examples


# NB: The examples below show a very basic modeling workflow. They have been 
# designed to work fast, not produce accurate, defensible models. They can
# take a few minutes to run.

library(mgcv)
library(sf)
library(terra)
set.seed(123)

### setup data
##############

# environmental rasters
rastFile <- system.file('extdata/madClim.tif', package='enmSdmX')
madClim <- rast(rastFile)

# coordinate reference system
wgs84 <- getCRS('WGS84')

# lemur occurrence data
data(lemurs)
occs <- lemurs[lemurs$species == 'Eulemur fulvus', ]
occs <- vect(occs, geom=c('longitude', 'latitude'), crs=wgs84)

occs <- elimCellDuplicates(occs, madClim)

occEnv <- extract(madClim, occs, ID = FALSE)
occEnv <- occEnv[complete.cases(occEnv), ]
	
# create 10000 background sites (or as many as raster can support)
bgEnv <- terra::spatSample(madClim, 20000)
bgEnv <- bgEnv[complete.cases(bgEnv), ]
bgEnv <- bgEnv[1:min(10000, nrow(bgEnv)), ]

# collate occurrences and background sites
presBg <- data.frame(
  presBg = c(
    rep(1, nrow(occEnv)),
    rep(0, nrow(bgEnv))
  )
)

env <- rbind(occEnv, bgEnv)
env <- cbind(presBg, env)

predictors <- c('bio1', 'bio12')

### calibrate models
####################

# Note that all of the trainXYZ functions can made to go faster using the
# "cores" argument (set to just 1, by default). The examples below will not
# go too much faster using more cores because they are simplified, but
# you can try!
cores <- 1

# MaxEnt
mx <- trainMaxEnt(
	data = env,
	resp = 'presBg',
	preds = predictors,
	regMult = 1, # too few values for reliable model, but fast
	verbose = TRUE,
	cores = cores
)

# MaxNet
mn <- trainMaxNet(
	data = env,
	resp = 'presBg',
	preds = predictors,
	regMult = 1, # too few values for reliable model, but fast
	verbose = TRUE,
	cores = cores
)

# generalized linear model (GLM)
gl <- trainGLM(
	data = env,
	resp = 'presBg',
	preds = predictors,
	scale = TRUE, # automatic scaling of predictors
	verbose = TRUE,
	cores = cores
)

# generalized additive model (GAM)
ga <- trainGAM(
	data = env,
	resp = 'presBg',
	preds = predictors,
	verbose = TRUE,
	cores = cores
)

# natural splines
ns <- trainNS(
	data = env,
	resp = 'presBg',
	preds = predictors,
	scale = TRUE, # automatic scaling of predictors
	df = 1:2, # too few values for reliable model(?)
	verbose = TRUE,
	cores = cores
)

# boosted regression trees
envSub <- env[1:1049, ] # subsetting data to run faster
brt <- trainBRT(
	data = envSub,
	resp = 'presBg',
	preds = predictors,
	learningRate = 0.001, # too few values for reliable model(?)
	treeComplexity = c(2, 3), # too few values for reliable model, but fast
	minTrees = 1200, # minimum trees for reliable model(?), but fast
	maxTrees = 1200, # too small for reliable model(?), but fast
	tryBy = 'treeComplexity',
	anyway = TRUE, # return models that did not converge
	verbose = TRUE,
	cores = cores
)

# random forests
rf <- trainRF(
	data = env,
	resp = 'presBg',
	preds = predictors,
	numTrees = c(100, 500), # using at least 500 recommended, but fast!
	verbose = TRUE,
	cores = cores
)

### make maps of models
#######################

# NB We do not have to scale rasters before predicting GLMs and NSs because we
# used the `scale = TRUE` argument in trainGLM() and trainNS().

mxMap <- predictEnmSdm(mx, madClim)
mnMap <- predictEnmSdm(mn, madClim) 
glMap <- predictEnmSdm(gl, madClim)
gaMap <- predictEnmSdm(ga, madClim)
nsMap <- predictEnmSdm(ns, madClim)
brtMap <- predictEnmSdm(brt, madClim)
rfMap <- predictEnmSdm(rf, madClim)

maps <- c(
	mxMap,
	mnMap,
	glMap,
	gaMap,
	nsMap,
	brtMap,
	rfMap
)

names(maps) <- c('MaxEnt', 'MaxNet', 'GLM', 'GAM', 'NSs', 'BRTs', 'RFs')
fun <- function() plot(occs, col='black', pch=3, add=TRUE)
plot(maps, fun = fun, nc = 4)

### compare model responses to BIO12 (mean annual precipitation)
################################################################

# make a data frame holding all other variables at mean across occurrences,
# varying only BIO12
occEnvMeans <- colMeans(occEnv, na.rm=TRUE)
occEnvMeans <- rbind(occEnvMeans)
occEnvMeans <- as.data.frame(occEnvMeans)
climFrame <- occEnvMeans[rep(1, 100), ]
rownames(climFrame) <- NULL

minBio12 <- min(env$bio12)
maxBio12 <- max(env$bio12)
climFrame$bio12 <- seq(minBio12, maxBio12, length.out=100)

predMx <- predictEnmSdm(mx, climFrame)
predMn <- predictEnmSdm(mn, climFrame)
predGl <- predictEnmSdm(gl, climFrame)
predGa <- predictEnmSdm(ga, climFrame)
predNat <- predictEnmSdm(ns, climFrame)
predBrt <- predictEnmSdm(brt, climFrame)
predRf <- predictEnmSdm(rf, climFrame)


plot(climFrame$bio12, predMx,
xlab='BIO12', ylab='Prediction', type='l', ylim=c(0, 1))

lines(climFrame$bio12, predMn, lty='solid', col='red')
lines(climFrame$bio12, predGl, lty='dotted', col='blue')
lines(climFrame$bio12, predGa, lty='dashed', col='green')
lines(climFrame$bio12, predNat, lty=4, col='purple')
lines(climFrame$bio12, predBrt, lty=5, col='orange')
lines(climFrame$bio12, predRf, lty=6, col='cyan')

legend(
   'topleft',
   inset = 0.01,
   legend = c(
	'MaxEnt',
	'MaxNet',
	'GLM',
	'GAM',
	'NS',
	'BRT',
	'RF'
   ),
   lty = c(1, 1:6),
   col = c(
	'black',
	'red',
	'blue',
	'green',
	'purple',
	'orange',
	'cyan'
   ),
   bg = 'white'
)
[Package enmSdmX version 1.1.6 Index]